How to Interpret GPR Images?
The supplementary material contains two sets of GPR (gene-protein-reaction) images.
The GPR images viewed from a gene perspective show the reactions associated with the
particular gene. The GPR images viewed from a reaction perspective show the genes
associated with a particular reaction. Both sets of images are useful for understanding
GPR associations. The following document will provide information on how to interpret
the GPR associations from the individual images.
For all views
1. Genes (cyan boxes) are designated by their gene locus name (or bnum), translated
peptides are represented as pink boxes, orange ovals represent functional proteins, and
blue boxes represent reactions labeled with the abbreviations listed in the supplementary
material.
2. Genes encoding protein subunits are associated with one protein. They are connected
by an “&” symbol in between the mRNA transcript and protein levels (see Figure 2 in
paper).
3. For protein complexes the proteins are connected by an “&” symbol in between the
protein and reaction levels (see Figure 2 in paper).
4. For isozymes, different proteins or protein complexes are connected to the same
reaction with different arrows. A reaction with two arrows coming into it indicates that
there are two isozymes (see Figure 2 in paper).
View by Gene
(filenames in the form gene_bxxx.jpg)
For a given locus (highlighted with a yellow box) the image will show:
1. All reactions which are associated with the selected gene.
2. Given this set of reactions it will also show all other enzymes and genes that are
associated with this set of reactions.
3. A red plus sign will appear next to one of these other proteins if it carries out a
reaction not associated with the selected gene. In other words, it indicates that the protein
carries out a reaction not shown in the image.
For the above GPR association, the gene aspC (locus b0928) is needed for the AspC
enzyme. This enzyme catalyzes the TYRTA, ASPTA, PHETA1 reactions. The TYRTA
and PHETA1 reactions can also be catalyzed by the enzyme TyrB (associated with the
b4054 locus). In addition the PHETA1 reaction can also be catalyzed by the IlvE enzyme
(associated with the b3770 locus). Both the IlvE and TyrB enzymes have red plus signs
next to them indicating that they also catalyze other reactions not associated with selected
gene aspC (b0928).
View by Reaction
(filenames in the form modelreactions_xxxx.jpg)
For a given reaction (highlighted with a yellow box) the image will show:
1. All proteins and genes associated with that reaction.
2. Given this set of proteins it will also show all other reactions catalyzed by these
proteins.
3. A red plus sign will appear next to a reaction if there are other proteins not shown in
the diagram which carry out this reaction (ie. isozymes) but do not carry out the selected
reaction.
4. A blue plus sign next to a protein indicates that it is involved in an enzyme complex
with one of the enzymes associated with the original reaction but is used to catalyze a
different reaction. The genes associated with these marked proteins are not shown.
5. A red plus sign next to a protein indicates that this protein is involved in the
catalysis of reaction not shown in the diagram.
The above image shows the GPR association for the reaction HISabc. The proteins HisJ,
HisM, HisP, and HisQ come together to form a protein complex, which carries out the
HISabc reaction. HisM, HisP, and HisQ also form a complex with ArgT which can carry
out the other three reactions, ORNabc, LYSabc, and ARGabc. Since ArgT isn’t involved
in the selected reaction HISabc, it is marked with a blue plus sign. The ARGabc reaction
is labeled with a red plus sign to indicate that there are other proteins (not shown) which
can carry out the same reaction.